Article: An Alternative Model of Amino Acid Replacement
G. E. Crooks, S. E. Brenner, Bioinformatics 21:975-980 (2005)
Abstract
We propose an alternative model of amino acid replacement during protein evolution. The observed correlations between pairs of homologous protein sequences are typically explained in terms of a Markovian dynamic of amino acid substitution. This model assumes that every location on the protein sequence has the same background distribution of amino acids, an assumption that is incompatible with the observed variation in amino acid composition across protein families and structural environments.
